A model has been developed for the digestion of organic matter in facultative ponds in tropical regions. Complete mixing has been assumed for the aerobic and anaerobic compartments. Settling, aerobic layer oxidation, and anaerobic layer methanogenesis are the main processes for organic matter removal in the water column. Exchange processes between layers are dispersive or soluble exchange, solubilization and transport of organic matter from sediments to water column are also taken into account. Degradation of organic matter in the sediments produces gaseous emissions to the water column. The exchange between bubbles ascending and the water column was measured. The model was calibrated with data obtained from a pilot facultative pond built in Muña Reservoir in Bogotá. The pond was sampled during 4 months to compare data between its water hyacinth covered section and uncovered section. The results clearly show the relative importance of different BOD removal processes in facultative ponds and suggest modifications to further improve performance. The results from the model suggest that internal loadings to facultative ponds due to solubilization and return of organic matter from the sediments to the aerobic layer greatly influence the soluble BOD effluent concentration. Aerobic degradation activity in the facultative pond does not affect significantly the effluent concentration. Anaerobic degradation activity in the facultative pond can more easily achieve increases in the removal efficiencies of BOD.